Concatipede requirements and workflow | How to use concatipede | Prepare the files | Set up the template for the correspondence table | Modify the correspondence table | Concatenate the alignents | Accessory functions | get_genbank_table() | rename_sequences() | Sequence names automatching
Package: concatipede 1.0.1
concatipede: Easy Concatenation of Fasta Sequences
Concatenation of multiple sequence alignments based on a correspondence table that can be edited in Excel <doi:10.5281/zenodo.5130603>.
Authors:
concatipede_1.0.1.tar.gz
concatipede_1.0.1.zip(r-4.7-any)concatipede_1.0.1.zip(r-4.6-any)concatipede_1.0.1.zip(r-4.5-any)
concatipede_1.0.1.tgz(r-4.6-any)concatipede_1.0.1.tgz(r-4.5-any)
concatipede_1.0.1.tar.gz(r-4.7-any)concatipede_1.0.1.tar.gz(r-4.6-any)
concatipede_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
concatipede/json (API)
| # Install 'concatipede' in R: |
| install.packages('concatipede', repos = c('https://tardipede.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tardipede/concatipede/issues
Pkgdown/docs site:https://tardipede.github.io
Last updated from:324e787c89. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 145 | ||
| source / vignettes | OK | 217 | ||
| linux-release | OK | 131 | ||
| macos-release | OK | 209 | ||
| macos-oldrel | OK | 210 | ||
| windows-devel | OK | 81 | ||
| windows-release | OK | 83 | ||
| windows-oldrel | OK | 91 | ||
| wasm-release | OK | 126 |
Exports:%>%auto_match_seqsconcatipedeconcatipede_exampleconcatipede_preparefind_fastaget_genbank_tableread_xlrename_sequenceswrite_fastawrite_nexuswrite_phylipwrite_xl
Dependencies:apecellrangerclicpp11crayondigestdplyrgenericsgluehmsigraphKernSmoothlatticelifecyclemagrittrMatrixnlmepillarpkgconfigprettyunitsprogressqualVR6Rcppreadxlrematchrlangstringdiststringistringrtibbletidyselectutf8vctrswithrwritexl
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build a template table with automatically matched sequence names | auto_match_seqs |
| Concatenate alignments | concatipede |
| Get the path to one of concatipede example files | concatipede_example |
| Load alignments and prepare template correspondence table for concatenate () function | concatipede_prepare |
| Find fasta files present in a folder | find_fasta |
| Extract GenBank accession number from correspondence table | get_genbank_table |
| Read an Excel file | read_xl |
| Rename sequences | rename_sequences |
| Writing alignments | write_aln write_fasta write_nexus write_phylip |
| Write an Excel file | write_xl |